Short Description

Ensemble of blocks that implement SODA method for confocal and super-resolution microscopy, in 2 and 3 dimensions

Team: Bio Image Analysis
Institution: Institut Pasteur
Website: http://icy.bioimageanalysis.org/

Documentation

This plugin contains 4 functional and independent blocks that performs SODA analysis in standard (widefield, confocal, structured-illumination…) and localization-based (STORM, PALM, DNA-PAINT…) microscopy. These blocks are called SODA, SODA storm 2D, SODA storm 3D and SODA suite. They are documented below.

Details of the method and algorithm are given in Mapping molecular assemblies with fluorescence microscopy and object-based spatial statistics (2018), Nature Communications. Please cite this article when using the SODA plugin.

Webinars about SODA

Advanced SMLM colocalization webinar from the NEUBIAS Academy (English). Part 2 by Thibault Lagache (at 00:47:39) is on Statistical tools for analyzing the spatial distribution of objects with a demo on the SODA plugin.

Colocalisation analysis with the Icy plugin SODA, webinar from the RT MFM network (French), with explanations on the SODA plugin

Block SODA for Icy Protocols

SODA block

Parameters of the block SODA

List of detections 1 & 2: spots (ROIs) corresponding to detections from channel or sequence 1 & 2

Input sequences: respective sequences of detections 1 & 2. Input sequences are used to compute the intensity centers (i.e. positions) of detections 1 & 2

ROI of analysis (cell’s shape) This key parameter corresponds to the ROI where SODA analysis is performed. If this ROI is too large, detections might appear as coupled (colocalized) while they are not..

Max. Radius and Step Max distance and step for computing the Ripley’s K function (see original article for details)

Fixed search distance: If selected, the plugin will simply count the number of detections 2 at distances 0, step,..,i*step,..Max. radius from detections 1

Output of the block SODA

The block SODA outputs a spreadsheet with the following values:

Sequence Name name of the processed image
Time time frame number
Nb detections 1 total number of detections 1 inside the selected ROIs of the image
Nb detections 2 total number of detections 2 inside the selected ROIs of the image
r 1 minimum distance used to compute the Ripley’s K function
r max maximum distance (max radius) used to compute the Ripley’s K function
Maximum of the K function max. value of the (reduced) Ripley’s K function over the different rings. It is used to compute the p-value of the null hypothesis (Poisson random distribution of detections 2)
p value log_10(p value) As the p-value is usually very small (<10^-10..), the log_10(p_value) is computed (otherwise, the p-value would be « equal » to 0 due to numerical approximations)
nb single 1 total number of spots in group 1 such that the coupling probability with any spot in group 2 is equal to 0
nb single 2 total number of spots in group 2 such that the coupling probability with any spot in group 1 is equal to 0
nb coupled 1 total number of spots 1 that are coupled (proba_coupling>0) with at least one spot 2
Mean number of partners 2 =nb coupled 2/nb coupled 1
nb coupled 2 total number of spots 2 that are coupled (proba_coupling>0) with at least one spot 1
Mean number of partners 1 =nb coupled 1/nb coupled 2
Mean coupling probability mean probability for two spots (one from group 1 and one from group 2) to be spatially coupled
Coupling index 1 sum_{x in spots 1, y in spots 2}(proba_coupling (x,y))/(total number of spots 1)  The coupling index gives an estimation of the “overlap” or the “association strength” between the two groups of spots
Coupling index 2 sum_{x in spots 2, y in spots 1}(proba_coupling (x,y))/(total number of spots 2)  The coupling index gives an estimation of the “overlap” or the “association strength” between the two groups of spots
Mean Coupling distance (pixels) mean distance between a spot from group 1 and a spot from group 2 that are coupled (ie spatially associated)

Protocols examples using the block SODA

Simple protocol screenshot

3 Color protocol

Block SODA STORM 2D

Protocols examples using the block SODA storm 2D

STORM 2D protocol

Blocks SODA STORM 3D

Protocols examples using the block SODA storm 3D

STORM 3D protocol and associated Demonstration video 1 (STORM imaging and analysis) and Demo video 2 (Using the SODA STORM 3D protocol)

Block SODA suite

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Changelog

  • Version 1.0.9.0 • Released on: 2020-12-10 11:00:00
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    Description:

    Fixed bug on workbook generation (Stephane)

  • Version 1.0.8.0 • Released on: 2020-11-02 00:00:00
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    Description:

    Fixed a bug about workbook editing

  • Version 1.0.7.0 • Released on: 2020-10-27 22:00:00
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    Description:

    Fixed bugs related to ROI infinity size (t=-1 & z=-1)
    (Thibault)

  • Version 1.0.6.0 • Released on: 2019-08-14 11:00:00
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    Description:

    Fixed plugins packaging so it correctly auto update (Stephane)

  • Version 1.0.5.0 • Released on: 2019-08-14 10:00:00
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    Description:

    Fixed issue with POI library update (Stephane)

  • Version 0.0.1.4 • Released on: 2018-08-12 21:48:23
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    Description:

    compatible with java 6

  • Version 0.0.1.3 • Released on: 2018-07-18 02:20:14
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    Description:

    Fixed some bugs on ROIs manipulation in Manders&Overlap coefficients computation (SODA suite bloc)

  • Version 0.0.1.2 • Released on: 2018-06-28 20:56:52
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  • Version 0.0.1.1 • Released on: 2018-02-28 22:25:42
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    Description:

    Fix bugs in trio block

  • Version 0.0.1.0 • Released on: 2018-02-23 18:30:02
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